Calcium in PDB 7mg5: Concanavalin A Bound to A Dna Glycoconjugate, Man-Atat

The structure of Concanavalin A Bound to A Dna Glycoconjugate, Man-Atat, PDB code: 7mg5 was solved by B.E.Partridge, P.H.Winegar, C.A.Mirkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.01 / 2.10
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	65.689, 70.7, 125.87, 90, 90, 90
R / Rfree (%)	20.1 / 24.5

The structure of Concanavalin A Bound to A Dna Glycoconjugate, Man-Atat also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Atat (pdb code 7mg5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Atat, PDB code: 7mg5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Atat


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Concanavalin A Bound to A Dna Glycoconjugate, Man-Atat within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:30.6 occ:1.00 O A:HOH436 2.3 28.3 1.0 OD2 A:ASP19 2.3 31.2 1.0 O A:TYR12 2.3 33.0 1.0 OD1 A:ASP10 2.3 29.7 1.0 O A:HOH442 2.4 28.8 1.0 OD1 A:ASN14 2.4 32.9 1.0 OD2 A:ASP10 2.4 24.4 1.0 CG A:ASP10 2.7 29.5 1.0 CG A:ASP19 3.4 34.9 1.0 C A:TYR12 3.5 33.8 1.0 CG A:ASN14 3.5 35.6 1.0 OD1 A:ASP19 3.9 35.2 1.0 N A:ASN14 4.1 34.9 1.0 MN A:MN301 4.1 34.8 1.0 CB A:ASN14 4.2 36.7 1.0 CB A:ASP10 4.2 30.3 1.0 O A:HOH415 4.3 29.1 1.0 CA A:TYR12 4.4 33.0 1.0 N A:TYR12 4.5 34.0 1.0 CE1 A:HIS24 4.5 32.2 1.0 N A:PRO13 4.5 35.1 1.0 O A:ASP208 4.5 27.2 1.0 CA A:PRO13 4.6 36.5 1.0 CB A:TYR12 4.6 33.5 1.0 C A:PRO13 4.6 36.6 1.0 ND2 A:ASN14 4.6 32.9 1.0 CB A:ASP19 4.7 36.1 1.0 O A:ARG228 4.7 28.7 1.0 CA A:ARG228 4.7 31.8 1.0 CB A:ARG228 4.7 33.5 1.0 OD2 A:ASP208 4.8 30.8 1.0 CA A:ASN14 4.8 34.7 1.0 NE2 A:HIS24 4.8 31.2 1.0 CD2 A:TYR12 5.0 33.1 1.0 CA A:ASP10 5.0 30.7 1.0

Calcium binding site 2 out of 2 in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Atat


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Concanavalin A Bound to A Dna Glycoconjugate, Man-Atat within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:31.2 occ:1.00 O B:HOH450 2.3 31.6 1.0 O B:TYR12 2.3 33.7 1.0 OD2 B:ASP19 2.3 33.0 1.0 OD1 B:ASP10 2.3 29.4 1.0 OD1 B:ASN14 2.4 39.3 1.0 O B:HOH448 2.4 35.6 1.0 OD2 B:ASP10 2.4 25.2 1.0 CG B:ASP10 2.7 29.0 1.0 CG B:ASP19 3.4 32.7 1.0 C B:TYR12 3.5 28.3 1.0 CG B:ASN14 3.5 41.8 1.0 OD1 B:ASP19 3.9 32.9 1.0 N B:ASN14 4.0 38.9 1.0 MN B:MN301 4.1 36.1 1.0 CB B:ASN14 4.2 38.3 1.0 CB B:ASP10 4.2 31.3 1.0 CA B:TYR12 4.3 30.7 1.0 N B:TYR12 4.4 30.5 1.0 N B:PRO13 4.4 32.2 1.0 CE1 B:HIS24 4.5 37.4 1.0 O B:HOH426 4.5 29.0 1.0 O B:ASP208 4.5 35.5 1.0 CB B:TYR12 4.5 31.5 1.0 CA B:PRO13 4.5 31.1 1.0 C B:PRO13 4.6 37.8 1.0 ND2 B:ASN14 4.6 41.0 1.0 CB B:ASP19 4.7 35.7 1.0 CB B:ARG228 4.7 32.9 1.0 OD2 B:ASP208 4.8 34.0 1.0 CA B:ARG228 4.8 32.1 1.0 CA B:ASN14 4.8 35.9 1.0 O B:ARG228 4.8 29.9 1.0 NE2 B:HIS24 4.8 36.4 1.0 CD2 B:TYR12 4.9 40.1 1.0

B.E.Partridge, P.H.Winegar, Z.Han, C.A.Mirkin. Redefining Protein Interfaces Within Protein Single Crystals with Dna J.Am.Chem.Soc. 2021.
ISSN: ESSN 1520-5126
DOI: 10.1021/JACS.1C04191